The Foundation was the first group to formally call for an ethics probe into an Alabama governor and his state-financed preaching (1991). Probable cause was found in the ethics probe. Scrutiny of the governor's record brought legal indictment.

A complaint by the Foundation expelled a preacher from the state docks in Mobile, Alabama, who was hired as a contractor using underage teenagers under his care at a Christian home as unpaid labor, in conditions that violated federal law (1989). The investigations started by the Foundation protest eventually closed down Bethel School in Mississippi (1990).

Foundation complaints have ended "grace" at public schools in Janesville, Wisconsin (1977); at the publicly-financed Independent Living, Madison, Wisconsin (1977); at Conway, Arkansas schools (1978). The Foundation halted paid prayers for at least one session in the Wisconsin Senate (1985). The Foundation has also ended school sponsorship of religious baccalaureates in several public school districts, such as in Monroe, Wisconsin (1989). The Foundation has widely circulated "The Case Against School Prayer" to many school districts around the nation. It has ended unlawful distribution of Gideon bibles in public schools.

In the "war of the bus ads," the Foundation began protesting "Keep Christ in Christmas" posters which were displayed free of charge on city buses in Madison, Wisconsin, in 1982. The free ads came down. In 1983 and 1984, the Foundation launched its own signs on Madison buses, reading: "The Bible: A Grim Fairy Tale" and a tongue-in-cheek cartoon showing Mary announcing, "It's a girl!"

In 1976, a complaint by co-founder Annie Laurie Gaylor, then a college student, ended a 122-year violation of prayers (invocations and benedictions) at University of Wisconsin-Madison graduation commencement ceremonies. (They haven't been missed!)